Bug 862273

Summary:	sci-biology/mothur-1.27.0-r1 fails to compile (lto): linearalgebra.cpp:1191:18: error: dereferencing type-punned pointer will break strict-aliasing rules [-Werror=strict-aliasing]
Product:	Gentoo Linux	Reporter:	Agostino Sarubbo <ago>
Component:	Current packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	RESOLVED FIXED
Severity:	normal
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Bug Depends on:
Bug Blocks:	618550
Attachments:	build.log

Description Agostino Sarubbo gentoo-dev

2022-07-30 08:30:01 UTC

https://blogs.gentoo.org/ago/2020/07/04/gentoo-tinderbox/

Issue: sci-biology/mothur-1.27.0-r1 fails to compile (lto).
Discovered on: amd64 (internal ref: lto_tinderbox)

NOTE:
This machine uses lto with CFLAGS=-flto -Werror=odr -Werror=lto-type-mismatch -Werror=strict-aliasing

Here is a bit of explanation:

-Werror=lto-type-mismatch:
User to find possible runtime issues in packages. It likely means the package is unsafe to build & use with LTO.
For projects using the same identifier but with different types across different files, they must be fixed to be consistent across the codebase.

-Werror=odr:
Used to find possible runtime issues in packages. These bugs are a problem anyway but may be even worse when combined with LTO. C++ code must comply with the One Definition Rule (ODR) - see https://en.cppreference.com/w/cpp/language/definition#One_Definition_Rule.

-Werror=strict-aliasing:
Used to find possible runtime issues in packages. These bugs are a problem anyway but may be even worse when combined with LTO.

Workarounds:
- If upstream is friendly and still active, file a bug upstream. For emulators, codecs, games, or multimedia packages, it may be worth just applying a workaround instead, as upstreams sometimes aren't receptive to these bugs (VALID FOR ALL).
- Use the new 'filter-lto' from flag-o-matic.eclass as it's likely to be unsafe with LTO (VALID FOR lto-type-mismatch - odr).
- Fix it yourself if interested, of course (VALID FOR ALL).
- Append-flags -fno-strict-aliasing (VALID FOR strict-aliasing).
- Use memcpy() but a union is sometimes suitable too (VALID FOR strict-aliasing).
- -fstrict-aliasing is implied by -O2, so this must be addressed in some form (VALID FOR strict-aliasing).

See also: https://marc.info/?l=gentoo-dev&m=165639574126280&w=2

Comment 1 Agostino Sarubbo gentoo-dev

2022-07-30 08:30:03 UTC

Created attachment 795757 [details]
build.log

build log and emerge --info

Comment 2 Sam James archtester

2022-07-30 08:35:24 UTC

It's pretty out of date.

Comment 3 Larry the Git Cow gentoo-dev

2024-03-22 08:43:53 UTC

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4aa71fb389486acee786f07025f7e24cfa07360a

commit 4aa71fb389486acee786f07025f7e24cfa07360a
Author:     Sam James <sam@gentoo.org>
AuthorDate: 2024-03-22 08:11:38 +0000
Commit:     Sam James <sam@gentoo.org>
CommitDate: 2024-03-22 08:43:28 +0000

    sci-biology/mothur: add 1.48.0
    
    Filter LTO too, and no-SA. Not reported upstream as it has a lot of open
    bugs already and seems low activity.
    
    Closes: https://bugs.gentoo.org/862273
    Signed-off-by: Sam James <sam@gentoo.org>

 sci-biology/mothur/Manifest                        |  1 +
 sci-biology/mothur/files/mothur-1.48.0-build.patch | 79 ++++++++++++++++++++++
 sci-biology/mothur/metadata.xml                    |  5 ++
 sci-biology/mothur/mothur-1.48.0.ebuild            | 54 +++++++++++++++
 4 files changed, 139 insertions(+)